Chapter 4 study guide

Question 1

The function of a protein depends on the detailed structure of

Answer 1

its 3-dimensional
shape

Question 2

A protein or polypeptide is a long chain of amino acids linked together by

Answer 2

covalent peptide bonds

Question 3

• The 20 different amino acids differ from one another in the chemical structure of their

Answer 3

side chains

Question 4

Protein folding is influenced by three types of…

Answer 4

non covalent bonds: hydrogen bonds, electrostatic interactions, and van der Waals

Question 5

Protein folding is also influenced by

Answer 5

hydophobic interactions (nonpolar side chains cluster together)

Question 6

Polar side chains tend to be found

Answer 6

on the outside surface

Question 7

The final folded structure or conformation of a polypeptide chain is usually determined
by its

Answer 7

lowest free energy state

Question 8

Proteins can be unfolded or denatured with solvents that

Answer 8

disrupt non-covalent
interactions

Question 9

When proteins fold incorrectly, they often form

Answer 9

insoluble aggregates

Question 10

Many neurodegenerative disorders are associated
with the formation of

Answer 10

protein aggregates

Question 11

Function of Protein aggregates

Answer 11

kill cells and tissues

Question 12

unusual type of neurodegenerative disease that is caused by infectious proteins that stimulate protein misfolding

Answer 12

Prion diseases

Question 13

Relatively easy now to determine a polypeptide sequence by sequencing

Answer 13

its gene

Question 14

The alpha helix and beta sheet are formed by

Answer 14

hydrogen bonds between N-H and C=O groups in the polypeptide backbone

Question 15

-the alpha helix (like a spiral staircase) forms a hydrogen bond between every __ amino acid, forming a regular helix with a turn every __ amino acids.

Answer 15

4th, 3.6

Question 16

alpha helices that span a membrane lipid bilayer typically have __ hydrophobic
amino acids that can contact the hydrophobic lipid tails

Answer 16

20

Question 17

some alpha helices can wrap around each other to form

Answer 17

coiled coils

Question 18

The hydrophobic amino acids on one side of an alpha-helix at positions ___ interact with the hydrophobic amino acids on one side of another alpha helix, whereas the hydrophilic amino acids can be exposed to the aqueous environment

Answer 18

a and d

Question 19

When the polypeptide strands run in the same direction (N to C terminal), they are called

Answer 19

parallel

Question 20

Most proteins contain small stretches of __ amino acids known as __ that can fold __ into a stable, compact structure.

Answer 20

100-250, protein
domains, independently

Question 21

The full three-dimensional structure of a polypeptide chain, with its multiple secondary
structures and domains, is considered its

Answer 21

tertiary structure

Question 22

If a protein molecule contains more than one polypeptide structure, this is known as its

Answer 22

quarternary structure

Question 23

A polypeptide that is n amino acids long would have __ potential amino acid sequences

Answer 23

20n

Question 24

Small changes in a polypeptide sequence (mutations) can disrupt protein structure and
function: what’s an example

Answer 24

Sickle cell anemia

Question 25

Protein families share...

Answer 25

both sequence and structural similarities, but differ in functions

Question 26

__ are a family of proteins that can cleave peptide bonds in a polypeptide chain.

Answer 26

serine proteases

Question 27

A binding site is any region on a protein surface that interacts with another molecule through

Answer 27

non-covalent bonds

Question 28

In larger protein complexes, each polypeptide chain is referred to as a

Answer 28

subunit

Question 29

Most proteins are

Answer 29

globular

Question 30

fold up into compact shapes like a ball with an irregular surface

Answer 30

globular proteins

Question 31

Collagen is composed of __ polypeptides that form a __ helix

Answer 31

3, triple

Question 32

The collagen molecules then bind end-to-end and side-to-side to form

Answer 32

Collagen fibrils

Question 33

The interactions between the collagen molecules are stabilized by

Answer 33

covalent bonds outside the cell

Question 34

There are many different kinds of covalent cross-links, but __ between the __ groups of __ are among the most common

Answer 34

disulfide bonds (S-S), SH of cytsesines

Question 35

These bonds are formed in the lumen of the ER

Answer 35

covalent cross links, S-S bonds

Question 36

Disulfide bonds are found in many

Answer 36

extracellular proteins, where they stabilize protein conformation

Question 37

Binding sites depend on the

Answer 37

3D organization of the polypeptide

Question 38

an example of proteins that bind their ligands with high affinity and specificity

Answer 38

Antibodies (IgG), ligands are antigens

Question 39

IgGs contain how many large and light chains

Answer 39

2 large and 2 light

Question 40

IgGs are held together by

Answer 40

S-S bonds

Question 41

Most of the polypeptide sequence is conserved between what region

Answer 41

constant regions

Question 42

the antigen-binding site is formed by

Answer 42

small variable loops in heavy and light chains

Question 43

Changing the length and sequence of the variable loops will alter

Answer 43

binding specificities for different antigens without affecting the structure of the rest of the antibody molecule

Question 44

breaks down polysaccharide chains in the cell walls of bacteria

Answer 44

Lysozyme

Question 45

Enzymes make and break

Answer 45

covalent bonds

Question 46

Many drugs work by blocking the activity of an

Answer 46

enzyme

Question 47

How are proteins controlled...

Answer 47

1. Regulate expression of the gene encoding the protein. 2. Target a protein to a specific cellular compartment 3. Alter protein degradation 4. Turn protein activities on and off by ligand bindings

Question 48

second sites where regulatory molecules can bind and alter protein conformation to either inactivate or stimulate a protein (or enzyme).

Answer 48

Allosteric regulation

Question 49

Examples of allosteric regulation

Answer 49

Feedback inhibition (neg and pos)

Question 50

major mechanism used by cells to control protein activity.

Answer 50

phosphorylation

Question 51

Phosphate groups contain

Answer 51

2 negative charges and their addition to serine, threonine, or tyrosine side chains alter protein conformation

Question 52

Phosphate addition is catalyzed by a

Answer 52

kinase

Question 53

Phosphates are removed from amino acid side chains by a

Answer 53

protein phosphatase

Question 54

Phosphorylation may either

Answer 54

stimulate or inhibit protein activity

Question 55

molecular switches that are regulated by the cyclic gain and loss of a phosphate group

Answer 55

GTP binding sites

Question 56

Use the energy of ATP binding, hydrolysis, and release to drive the conformational changes needed to move in one direction along a track are done by what proteins

Answer 56

Motor proteins

Question 57

Ex of motor proteins

Answer 57

myosin moving on an actin filament, kinesin moving on microtubules, DNA polymerase moving on a DNA strand.

Question 58

Proteins often form large machines with

Answer 58

10 or more subunits

Question 59

contain binding sites that are recognized by multiple proteins

Answer 59

scaffold proteins

Question 60

Binding of several proteins to a scaffold enables formation of

Answer 60

protein complex

Question 61

__ modifications of amino acids after __ also control the location and assembly of protein machines

Answer 61

covalent, translation

Question 62

Addition of the __ drives proteins to cell membranes

Answer 62

palmitate to cysteines

Question 63

The set of covalent modifications that a protein contains is an important way of regulating the protein’s function and constitutes a

Answer 63

regulatory protein code

Question 64

To isolate a protein from a particular cell type, one must break open the cell (poke holes in the cell membrane) to make a

Answer 64

cell homogenate or extract that contains all the cell organelles

Question 65

There are several methods commonly used in cell fractionation and centrifugation

Answer 65

a) sonication (high frequency sound) b) mild detergent treatment c) forcing cells through small holes under high pressure d) mechanical shear

Question 66

Once you have your cell extract, you can separate it into crude fractions by

Answer 66

differential centrifugation

Question 67

Less dense components of centrifuge settle at

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the bottom more quickly

Question 68

Centrifugation: contains whole cells, partially disrupted cells (cell ghosts), and nuclei

Answer 68

low speed pellet

Question 69

contains the larger organelles (mitochondria, lysosomes, peroxisomes)

Answer 69

medium speed pellet

Question 70

contains the larger organelles (mitochondria, lysosomes, peroxisomes)

Answer 70

high speed pellet

Question 71

contains large cytoplasmic protein complexes (ribosomes, virus particles, large macromolecules)

Answer 71

very high speed pellet

Question 72

Typically used to separate larger protein complexes based on the rates that they move through a shallow gradient of sucrose.

Answer 72

Velocity sedimentation

Question 73

Larger, denser complexes will move __ than smaller, less dense complexes

Answer 73

faster

Question 74

used to separate components based on their buoyant density, independent of size and shape.

Answer 74

Equilibrium centrifugation

Question 75

often used to isolate nucleic acids (DNA, RNA)

Answer 75

Equilibrium centrifugation

Question 76

separates proteins according to their size

Answer 76

Gel filtration chromatography

Question 77

separate the crude protein mixture on the basis of size, charge, and/or its ability to bind to a particular chemical group

Answer 77

Column chromatography

Question 78

contain a matrix that is covalently bound to a molecule that interacts specifically with the protein of interest

Answer 78

Affinity columns

Question 79

This molecule may resemble an enzyme’s substrate, or it might be a specific antibody that recognizes an antigen on the protein surface

Answer 79

Affinity columns

Question 80

the proteins are treated with a negatively charged detergent, sodium dodecyl sulfate (SDS), which denatures the proteins, and a reducing agent, which breaks disulfide bonds

Answer 80

SDS polyacrylamide gel electrophoresis (SDS-PAGE)

Question 81

the gel contains a pH gradient, and the proteins are NOT treated with SDS. Proteins will migrate in the pH gradient until they reach their individual isoelectric points

Answer 81

isoelectric focusing gel

Question 82

mixtures of proteins will be separated in the first dimension by isoelectric focusing, and then the gel will be treated with SDS and run in the second dimension using SDS-PAGE

Answer 82

two-dimensional gel electrophoresis

Question 83

If you have a complex mixture of proteins, you can sometimes identify what proteins are in that mixture using

Answer 83

mass sepctrometry

Question 84

to determine the structure of large protein complexes, integral membrane proteins and dynamic proteins. This technique involves rapidly freezing the proteins and exposing them to a beam of electrons, which projects the images of the molecules onto a detector.

Answer 84

Cryoelectron microscopy